This is normal behavior. It is time for the cygnets to leave prior to the next breeding season. More than likely, the cygnet being dispatched early is the oldest swan and a male. He is now seen as a rival to the male parent.

Although this is normal behavior, you may need to find the cygnet another safe home as if he is not able to access food and water without being chased, he will get very stressed and succumb to stress-induced injury or illness. If your pond/habitat is large enough to fence off, you may need to divide the habitat. However, this is not going to solve the overall problem as you are going to to have this same problem on an annual basis due to the swans having cygnets yearly for the rest of their lives. Double this problem if the young male takes up with his younger sister (can and does normally happen without any genetic anomalies) and produces cygnets on an annual basis. The Regal Swan